Coastal bays in the Caribbean accommodate different marine ecosystems, including seagrass meadows and coral reefs, which provide important ecosystem services. However, these marine ecosystems are endangered. Seagrass ecosystems have a key role in coastal bays, but despite their alarming rates of loss, they receive little attention compared to other marine ecosystems. This study aims to provide a better understanding of the role of seagrass ecosystems in coastal bays by assessing their impact on the morphodynamic behavior. In order to achieve this, an existing hydrodynamic model has been extended to include morphodynamics. Two different bays have been investigated: Baie Orientale and Baie de l’Embouchure (St. Martin). These bays represent a partially exposed and fully sheltered bay, respectively. Both regular wave conditions, as well as extreme storm conditions, have been investigated to understand the consequences of seagrass loss on coastal erosion for different environmental climates. The coastal erosion has been found to be more prominent in the exposed region, whereas the more sheltered areas are more resilient. The erosion takes place in shallow waters but remains limited under regular swell conditions. The increased wave energy, during the extreme storm event, increases the erosion rates considerably. However, the regular swell conditions are normative in shaping the morphological development of these coastal bays when longer timescales are considered. The seagrass counters erosion most effectively in the foreshore and much less in deeper regions. Removal of seagrass in the foreshore (between 1-3m) halves the sediment stabilization. In contrast, the sediment stabilization increases if the meadows are able to spread especially towards the shore. In addition, the wave energy and waveform have a significant impact on the sediment stabilization. The stabilization typically decreases for higher and shorter (storm) waves, whereas it increases for smaller and longer (swell) waves. The long-distance interactions between seagrass meadows and coral reefs have led to their mutual coexistence, which is also found to be beneficial for the erosion control of the coastal bays. The dissipation of wave energy on top of the reefs fosters the sediment stabilization by seagrass. Moreover, the impact of the reefs on sediment stabilization also increases in the presence of seagrass meadows due to the additional drag exerted by the seagrass. The seagrass meadows are typically more effective under swell waves, whereas the reefs are more dominant in the dissipation of storm waves. Seagrass meadows and coral reefs form thus a synergy, in which the stabilization of sediments provided by the individual ecosystems is facilitated, reinforced, and complemented by the proximate presence of the other ecosystem. Finally, the role of seagrass on sediment stabilization has been explored under climate change. The coastal erosion increases for the considered sea-level rise scenarios. The impact of the seagrass on sediment stabilization decreases when the bays, seagrass and reef ecosystems are not able to keep up with sea-level rise. The synergy between seagrass and reefs emphasizes that the responses of both ecosystems are of importance for the future of tropical sheltered bays and should therefore not be managed in isolation.